Code used for the analysis of the RNA-seq, ATAC-seq and ChIP-seq datasets produced in this study. Original fastq files deposited in https://ega-archive.org/, under the accession number EGAD00001009288.
Different folders are included in this repository:
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RNA-seq folder: contains all the code used for RNA-seq analysis. Two different datasets were analyzed: time course differentiation of mDAN, including smNPC and Astrocytes at day 65 of differentiation, and TF KD samples.
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ATAC-seq folder: contains all the code used for ATAC-seq analysis of the time course data. Remember that ATAC and RNA sequencing are paired samples. Used the date especified either in the fastq or csv files to associate both datasets
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ChIP-seq folder: contains all the code used for ChIP-seq analysis. Take into account that although single-end sequencing was used, R1 and R2 fastq files are available per sample. Please check the guidelines of Active Motif to understand why (https://www.activemotif.com/documents/2056.pdf)
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EPIC-DREM folder: contains all the code used for running EPIC-DREM. EPIC-DREM integrated ATAC and RNA-seq paired datasets